Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium

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• 作者：Mingquan Ding (1) (2)
  Jiadong Chen (1)
  Yurong Jiang (1)
  Lifeng Lin (3)
  YueFen Cao (1)
  Minhua Wang (1)
  Yuting Zhang (1)
  Junkang Rong (1) (2)
  Wuwei Ye (2)
  
• 关键词：WRKY gene family ; G. raimondii ; Genome wide analysis ; Fiber development
• 刊名：Molecular Genetics and Genomics
• 出版年：2015
• 出版时间：February 2015
• 年：2015
• 卷：290
• 期：1
• 页码：151-171
• 全文大小：4,339 KB
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• 作者单位：Mingquan Ding (1) (2)
  Jiadong Chen (1)
  Yurong Jiang (1)
  Lifeng Lin (3)
  YueFen Cao (1)
  Minhua Wang (1)
  Yuting Zhang (1)
  Junkang Rong (1) (2)
  Wuwei Ye (2)
  
  1. The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China
  2. State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
  3. Nanosphere Inc, 4088 Commercial Drive, Northbrook, IL, 60062, USA
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Biochemistry
  Microbial Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1617-4623

文摘

WRKY transcription factors play important roles in various stress responses in diverse plant species. In cotton, this family has not been well studied, especially in relation to fiber development. Here, the genomes and transcriptomes of Gossypium raimondii and Gossypium arboreum were investigated to identify fiber development related WRKY genes. This represents the first comprehensive comparative study of WRKY transcription factors in both diploid A and D cotton species. In total, 112 G. raimondii and 109 G. arboreum WRKY genes were identified. No significant gene structure or domain alterations were detected between the two species, but many SNPs distributed unequally in exon and intron regions. Physical mapping revealed that the WRKY genes in G. arboreum were not located in the corresponding chromosomes of G. raimondii, suggesting great chromosome rearrangement in the diploid cotton genomes. The cotton WRKY genes, especially subgroups I and II, have expanded through multiple whole genome duplications and tandem duplications compared with other plant species. Sequence comparison showed many functionally divergent sites between WRKY subgroups, while the genes within each group are under strong purifying selection. Transcriptome analysis suggested that many WRKY genes participate in specific fiber development processes such as fiber initiation, elongation and maturation with different expression patterns between species. Complex WRKY gene expression such as differential Dt and At allelic gene expression in G. hirsutum and alternative splicing events were also observed in both diploid and tetraploid cottons during fiber development process. In conclusion, this study provides important information on the evolution and function of WRKY gene family in cotton species.